esys.modellib.visualization Package¶
Classes¶
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class
esys.modellib.visualization.Data¶ Bases:
Boost.Python.instanceRepresents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.
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__init__((object)arg1) → None¶ __init__( (object)arg1, (object)value [, (object)p2 [, (object)p3 [, (object)p4]]]) -> None
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conjugate((Data)arg1) → Data¶
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copy((Data)arg1, (Data)other) → None :¶ Make this object a copy of
othernote: The two objects will act independently from now on. That is, changing otherafter this call will not change this object and vice versa.- copy( (Data)arg1) -> Data :
note: In the no argument form, a new object will be returned which is an independent copy of this object.
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copyWithMask((Data)arg1, (Data)other, (Data)mask) → None :¶ Selectively copy values from
otherData.Datapoints which correspond to positive values inmaskwill be copied fromotherParameters:
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delay((Data)arg1) → Data :¶ Convert this object into lazy representation
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dump((Data)arg1, (str)fileName) → None :¶ Save the data as a netCDF file
Parameters: fileName ( string) –
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expand((Data)arg1) → None :¶ Convert the data to expanded representation if it is not expanded already.
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getDomain((Data)arg1) → Domain :¶ Return type: Domain
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getFunctionSpace((Data)arg1) → FunctionSpace :¶ Return type: FunctionSpace
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getNumberOfDataPoints((Data)arg1) → int :¶ Return type: intReturns: Number of datapoints in the object
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getRank((Data)arg1) → int :¶ Returns: the number of indices required to address a component of a datapoint Return type: positive int
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getShape((Data)arg1) → tuple :¶ Returns the shape of the datapoints in this object as a python tuple. Scalar data has the shape
()Return type: tuple
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getTagNumber((Data)arg1, (int)dpno) → int :¶ Return tag number for the specified datapoint
Return type: int Parameters: dpno (int) – datapoint number
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getTupleForDataPoint((Data)arg1, (int)dataPointNo) → object :¶ Returns: Value of the specified datapoint Return type: tupleParameters: dataPointNo ( int) – datapoint to access
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getTupleForGlobalDataPoint((Data)arg1, (int)procNo, (int)dataPointNo) → object :¶ Get a specific datapoint from a specific process
Return type: tupleParameters: - procNo (positive
int) – MPI rank of the process - dataPointNo (int) – datapoint to access
- procNo (positive
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hasInf((Data)arg1) → bool :¶ Returns return true if data contains +-Inf. [Note that for complex values, hasNaN and hasInf are not mutually exclusive.]
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hasNaN((Data)arg1) → bool :¶ Returns return true if data contains NaN. [Note that for complex values, hasNaN and hasInf are not mutually exclusive.]
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imag((Data)arg1) → Data¶
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internal_maxGlobalDataPoint((Data)arg1) → tuple :¶ Please consider using getSupLocator() from pdetools instead.
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internal_minGlobalDataPoint((Data)arg1) → tuple :¶ Please consider using getInfLocator() from pdetools instead.
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interpolate((Data)arg1, (FunctionSpace)functionspace) → Data :¶ Interpolate this object’s values into a new functionspace.
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interpolateTable((Data)arg1, (object)table, (float)Amin, (float)Astep, (Data)B, (float)Bmin, (float)Bstep[, (float)undef=1e+50[, (bool)check_boundaries=False]]) → Data :¶ - Creates a new Data object by interpolating using the source data (which are
looked up in
table)Amust be the outer dimension on the tableparam table: two dimensional collection of values param Amin: The base of locations in table type Amin: float param Astep: size of gap between each item in the table type Astep: float param undef: upper bound on interpolated values type undef: float param B: Scalar representing the second coordinate to be mapped into the table type B: Dataparam Bmin: The base of locations in table for 2nd dimension type Bmin: float param Bstep: size of gap between each item in the table for 2nd dimension type Bstep: float param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used. raise RuntimeError(DataException): if the coordinates do not map into the table or if the interpolated value is above undefrtype: Data
interpolateTable( (Data)arg1, (object)table, (float)Amin, (float)Astep [, (float)undef=1e+50 [, (bool)check_boundaries=False]]) -> Data
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isComplex((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datastores complex values.
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isConstant((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datais an instance ofDataConstantNote: This does not mean the data is immutable.
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isEmpty((Data)arg1) → bool :¶ Is this object an instance of
DataEmptyReturn type: boolNote: This is not the same thing as asking if the object contains datapoints.
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isExpanded((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datais expanded.
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isLazy((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datais lazy.
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isProtected((Data)arg1) → bool :¶ Can this instance be modified. :rtype:
bool
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isReady((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datais not lazy.
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isTagged((Data)arg1) → bool :¶ Return type: boolReturns: True if this Datais expanded.
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nonuniformInterpolate((Data)arg1, (object)in, (object)out, (bool)check_boundaries) → Data :¶ 1D interpolation with non equally spaced points
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nonuniformSlope((Data)arg1, (object)in, (object)out, (bool)check_boundaries) → Data :¶ 1D interpolation of slope with non equally spaced points
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phase((Data)arg1) → Data¶
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promote((Data)arg1) → None¶
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real((Data)arg1) → Data¶
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replaceInf((Data)arg1, (object)value) → None :¶ Replaces +-Inf values with value. [Note, for complex Data, both real and imaginary components are replaced even if only one part is Inf].
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replaceNaN((Data)arg1, (object)value) → None :¶ Replaces NaN values with value. [Note, for complex Data, both real and imaginary components are replaced even if only one part is NaN].
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resolve((Data)arg1) → None :¶ Convert the data to non-lazy representation.
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setProtection((Data)arg1) → None :¶ Disallow modifications to this data object
Note: This method does not allow you to undo protection.
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setTaggedValue((Data)arg1, (int)tagKey, (object)value) → None :¶ Set the value of tagged Data.
param tagKey: tag to update type tagKey: int- setTaggedValue( (Data)arg1, (str)name, (object)value) -> None :
param name: tag to update type name: stringparam value: value to set tagged data to type value: objectwhich acts like an array,tupleorlist
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setToZero((Data)arg1) → None :¶ After this call the object will store values of the same shape as before but all components will be zero.
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setValueOfDataPoint((Data)arg1, (int)dataPointNo, (object)value) → None¶ setValueOfDataPoint( (Data)arg1, (int)arg2, (object)arg3) -> None
setValueOfDataPoint( (Data)arg1, (int)arg2, (float)arg3) -> None :
Modify the value of a single datapoint.
param dataPointNo: type dataPointNo: int param value: type value: floator an object which acts like an array,tupleorlistwarning: Use of this operation is discouraged. It prevents some optimisations from operating.
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tag((Data)arg1) → None :¶ Convert data to tagged representation if it is not already tagged or expanded
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toListOfTuples((Data)arg1[, (bool)scalarastuple=False]) → object :¶ Return the datapoints of this object in a list. Each datapoint is stored as a tuple.
Parameters: scalarastuple – if True, scalar data will be wrapped as a tuple. True => [(0), (1), (2)]; False => [0, 1, 2]
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class
esys.modellib.visualization.Link(target, attribute=None)¶ Bases:
objectA Link makes an attribute of an object callable:
o.object() o.a=8 l=Link(o,"a") assert l()==8
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__init__(target, attribute=None)¶ Creates a link to the object target. If attribute is given, the link is established to this attribute of the target. Otherwise the attribute is undefined.
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classmethod
fromDom(esysxml, node)¶
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getAttributeName()¶ Returns the name of the attribute the link is pointing to.
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getTarget()¶ Returns the target.
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hasDefinedAttributeName()¶ Returns true if an attribute name is set.
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setAttributeName(attribute)¶ Sets a new attribute name to be collected from the target object. The target object must have the attribute with name attribute.
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toDom(esysxml, node)¶ toDommethod of Link. Creates a Link node and appends it to the current XML esysxml.
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class
esys.modellib.visualization.Model(parameters=[], **kwargs)¶ Bases:
esys.escriptcore.modelframe.ParameterSetA Model object represents a process marching over time until a finalizing condition is fulfilled. At each time step an iterative process can be performed and the time step size can be controlled. A Model has the following work flow:
doInitialization() while not terminateInitialIteration(): doInitialStep() doInitialPostprocessing() while not finalize(): dt=getSafeTimeStepSize(dt) doStepPreprocessing(dt) while not terminateIteration(): doStep(dt) doStepPostprocessing(dt) doFinalization()
where
doInitialization,finalize,getSafeTimeStepSize,doStepPreprocessing,terminateIteration,doStepPostprocessing,doFinalizationare methods of the particular instance of a Model. The default implementations of these methods have to be overwritten by the subclass implementing a Model.-
__init__(parameters=[], **kwargs)¶ Creates a model.
Just calls the parent constructor.
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UNDEF_DT= 1e+300¶
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checkLinkTargets(models, hash)¶ Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.
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declareParameter(**parameters)¶ Declares one or more new parameters and their initial value.
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declareParameters(parameters)¶ Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.
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doFinalization()¶ Finalizes the time stepping.
This function may be overwritten.
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doInitialPostprocessing()¶ Finalises the initialization iteration process. This method is not called in case of a restart.
This function may be overwritten.
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doInitialStep()¶ Performs an iteration step in the initialization phase. This method is not called in case of a restart.
This function may be overwritten.
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doInitialization()¶ Initializes the time stepping scheme. This method is not called in case of a restart.
This function may be overwritten.
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doStep(dt)¶ Executes an iteration step at a time step.
dtis the currently used time step size.This function may be overwritten.
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doStepPostprocessing(dt)¶ Finalises the time step.
dt is the currently used time step size.
This function may be overwritten.
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doStepPreprocessing(dt)¶ Sets up a time step of step size dt.
This function may be overwritten.
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finalize()¶ Returns False if the time stepping is finalized.
This function may be overwritten.
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classmethod
fromDom(esysxml, node)¶
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getAttributeObject(name)¶ Returns the object stored for attribute
name.
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getSafeTimeStepSize(dt)¶ Returns a time step size which can be safely used.
dtgives the previously used step size.This function may be overwritten.
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hasAttribute(name)¶ Returns True if self has attribute
name.
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releaseParameters(name)¶ Removes parameter name from the parameters.
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setUp()¶ Sets up the model.
This function may be overwritten.
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showParameters()¶ Returns a description of the parameters.
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terminateInitialIteration()¶ Returns True if iteration at the inital phase is terminated.
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terminateIteration()¶ Returns True if iteration on a time step is terminated.
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toDom(esysxml, node)¶ toDommethod of Model class.
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trace(msg)¶ If debugging is on, prints the message, otherwise does nothing.
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writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶ Writes the object as an XML object into an output stream.
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class
esys.modellib.visualization.Visualization(**kwargs)¶ Bases:
esys.escriptcore.modelframe.ModelGeneric visualization Model
Variables: - t – current time (in)
- n – frame counter (in)
- dt – increment for output (in)
- filename – name of the output file (in)
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__init__(**kwargs)¶ Initialisation of the visualisation model object
Parameters: debug – Debugging flag
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UNDEF_DT= 1e+300¶
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checkLinkTargets(models, hash)¶ Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.
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declareParameter(**parameters)¶ Declares one or more new parameters and their initial value.
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declareParameters(parameters)¶ Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.
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doFinalization()¶ Finalizes the time stepping.
This function may be overwritten.
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doInitialPostprocessing()¶ Finalises the initialization iteration process. This method is not called in case of a restart.
This function may be overwritten.
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doInitialStep()¶ Performs an iteration step in the initialization phase. This method is not called in case of a restart.
This function may be overwritten.
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doInitialization()¶ does some kind of initialisation
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doStep(dt)¶ Executes an iteration step at a time step.
dtis the currently used time step size.This function may be overwritten.
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doStepPostprocessing(dt)¶ Finalises the time step.
dt is the currently used time step size.
This function may be overwritten.
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doStepPreprocessing(dt)¶ Sets up a time step of step size dt.
This function may be overwritten.
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finalize()¶ Returns False if the time stepping is finalized.
This function may be overwritten.
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classmethod
fromDom(esysxml, node)¶
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getAttributeObject(name)¶ Returns the object stored for attribute
name.
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getFrameCounter()¶ returns a frame counter
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getFrameFileName()¶
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getSafeTimeStepSize(dt)¶ returns new step size
Parameters: dt ( float) – last time step size usedReturns: time step size that can savely be used Return type: float
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hasAttribute(name)¶ Returns True if self has attribute
name.
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releaseParameters(name)¶ Removes parameter name from the parameters.
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setUp()¶ Sets up the model.
This function may be overwritten.
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showParameters()¶ Returns a description of the parameters.
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terminateInitialIteration()¶ Returns True if iteration at the inital phase is terminated.
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terminateIteration()¶ Returns True if iteration on a time step is terminated.
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toDom(esysxml, node)¶ toDommethod of Model class.
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trace(msg)¶ If debugging is on, prints the message, otherwise does nothing.
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writeFrame()¶ returns True if the time stamp for writing frame is reached.
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writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶ Writes the object as an XML object into an output stream.
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class
esys.modellib.visualization.WriteVTK(**kwargs)¶ Bases:
esys.modellib.visualization.VisualizationWrites data into a VTK file.
The Model can handel up to 20 data sets that are written into a single file tagged with the given name. If no name is given and the data are defined by a
Linkthe name of the target attribute is used as a tag.Variables: - data0 – data set 0 to be written
- name0 – name tag for data set 0
- data1 – data set 1 to be written
- name1 – name tag for data set 1
- data2 – data set 2 to be written
- name2 – name tag for data set 2
- data3 – data set 3 to be written
- name3 – name tag for data set 3
- data4 – data set 4 to be written
- name4 – name tag for data set 4
- data5 – data set 5 to be written
- name5 – name tag for data set 5
- data6 – data set 6 to be written
- name6 – name tag for data set 6
- data7 – data set 7 to be written
- name7 – name tag for data set 7
- data8 – data set 8 to be written
- name8 – name tag for data set 8
- data9 – data set 9 to be written
- name9 – name tag for data set 9
- data10 – data set 10 to be written
- name10 – name tag for data set 10
- data11 – data set 11 to be written
- name11 – name tag for data set 11
- data12 – data set 12 to be written
- name12 – name tag for data set 12
- data13 – data set 13 to be written
- name13 – name tag for data set 13
- data14 – data set 14 to be written
- name14 – name tag for data set 14
- data15 – data set 15 to be written
- name15 – name tag for data set 15
- data16 – data set 16 to be written
- name16 – name tag for data set 16
- data17 – data set 17 to be written
- name17 – name tag for data set 17
- data18 – data set 18 to be written
- name18 – name tag for data set 18
- data19 – data set 19 to be written
- name19 – name tag for data set 19
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__init__(**kwargs)¶ Initialisation of the WriteVTK object
Parameters: debug ( bool) – debugging flag
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UNDEF_DT= 1e+300¶
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checkLinkTargets(models, hash)¶ Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.
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collectData()¶
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declareParameter(**parameters)¶ Declares one or more new parameters and their initial value.
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declareParameters(parameters)¶ Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.
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doFinalization()¶ Finalizes the time stepping.
This function may be overwritten.
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doInitialPostprocessing()¶ writes vtk file at the end of initial iteration
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doInitialStep()¶ Performs an iteration step in the initialization phase. This method is not called in case of a restart.
This function may be overwritten.
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doInitialization()¶ does some kind of initialisation
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doStep(dt)¶ Executes an iteration step at a time step.
dtis the currently used time step size.This function may be overwritten.
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doStepPostprocessing(dt)¶ writes vtk file at the end of time iteration
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doStepPreprocessing(dt)¶ Sets up a time step of step size dt.
This function may be overwritten.
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finalize()¶ Returns False if the time stepping is finalized.
This function may be overwritten.
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classmethod
fromDom(esysxml, node)¶
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getAttributeObject(name)¶ Returns the object stored for attribute
name.
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getFrameCounter()¶ returns a frame counter
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getFrameFileName()¶
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getSafeTimeStepSize(dt)¶ returns new step size
Parameters: dt ( float) – last time step size usedReturns: time step size that can savely be used Return type: float
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hasAttribute(name)¶ Returns True if self has attribute
name.
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releaseParameters(name)¶ Removes parameter name from the parameters.
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setUp()¶ Sets up the model.
This function may be overwritten.
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showParameters()¶ Returns a description of the parameters.
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terminateInitialIteration()¶ Returns True if iteration at the inital phase is terminated.
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terminateIteration()¶ Returns True if iteration on a time step is terminated.
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toDom(esysxml, node)¶ toDommethod of Model class.
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trace(msg)¶ If debugging is on, prints the message, otherwise does nothing.
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writeFrame()¶ returns True if the time stamp for writing frame is reached.
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writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶ Writes the object as an XML object into an output stream.
Functions¶
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esys.modellib.visualization.saveVTK(filename, domain=None, metadata='', metadata_schema=None, write_meshdata=False, time=0.0, cycle=0, **data)¶ Writes
Dataobjects and their mesh to a file using the VTK XML file format.Example:
temp=Scalar(..) v=Vector(..) saveVTK("solution.vtu", temperature=temp, velocity=v)
tempandvare written to “solution.vtu” wheretempis named “temperature” andvis named “velocity”.Meta tags, e.g. a timeStamp, can be added to the file, for instance:
tmp=Scalar(..) v=Vector(..) saveVTK("solution.vtu", temperature=tmp, velocity=v, metadata="<timeStamp>1.234</timeStamp>", metadata_schema={"gml":"http://www.opengis.net/gml"})
The argument
metadata_schemaallows the definition of name spaces with a schema used in the definition of meta tags.Parameters: - filename (
str) – name of the output file (‘.vtu’ is added if required) - domain (
escript.Domain) – domain of theDataobjects. If not specified, the domain of the givenDataobjects is used. - <name> – writes the assigned value to the VTK file using <name> as identifier
- metadata (
str) – additional XML meta data which are inserted into the VTK file. The meta data are marked by the tag<MetaData>. - metadata_schema (
dictwithmetadata_schema[<namespace>]=<URI>to assign the scheme<URI>to the name space<namespace>.) – assigns schemas to namespaces which have been used to define meta data. - write_meshdata (
bool) – whether to save mesh-related data such as element identifiers, ownership etc. This is mainly useful for debugging. - time (
float) – the timestamp to save within the file, seperate to metadata - cycle (
int) – the cycle (or timestep) of the data
Note: All data objects have to be defined on the same domain. They may not be in the same
FunctionSpacebut not all combinations ofFunctionSpaces can be written to a single VTK file. Typically, data on the boundary and on the interior cannot be mixed.- filename (